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Misc fixes #94

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merged 5 commits into from
Oct 5, 2023
Merged

Misc fixes #94

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38e330c
Remove CmdStanPy installation from GH
gibsramen Oct 4, 2023
fa63945
README fixes
gibsramen Oct 4, 2023
3790c54
Clean up testing
gibsramen Oct 4, 2023
32e37f6
Add coverage reports
gibsramen Oct 4, 2023
f7cf4b2
Update main.yml
gibsramen Oct 4, 2023
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13 changes: 3 additions & 10 deletions .github/workflows/main.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -39,23 +39,16 @@ jobs:

- name: Install conda packages
shell: bash -l {0}
run: mamba install -c conda-forge biom-format patsy pytest xarray scikit-bio flake8 arviz

# Temp req before CmdStanPy cuts a new release
- name: Install develop branch of CmdStanPy
shell: bash -l {0}
run: >
pip install git+https://github.com/stan-dev/cmdstanpy.git@develop;
install_cmdstan
run: mamba install -c conda-forge biom-format patsy pytest xarray scikit-bio flake8 arviz cmdstanpy pytest-cov

- name: Install BIRDMAn
shell: bash -l {0}
run: pip install -e .[dev]

- name: Check style
shell: bash -l {0}
run: flake8 birdman/*.py tests/*.py setup.py
run: make stylecheck

- name: Run tests
shell: bash -l {0}
run: pytest --disable-pytest-warnings
run: make pytest
1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -17,3 +17,4 @@ tests/custom_model
/build
docs/_build
tags
.coverage*
2 changes: 1 addition & 1 deletion Makefile
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Expand Up @@ -6,7 +6,7 @@ stylecheck:
flake8 birdman/*.py tests/*.py setup.py

pytest:
pytest tests -W ignore::FutureWarning
pytest --cov-report term-missing --cov=birdman --cov-branch tests

documentation:
cd docs && make html
6 changes: 4 additions & 2 deletions README.md
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@@ -1,6 +1,6 @@
# BIRDMAn

[![GitHub Actions CI](https://github.com/gibsramen/birdman/workflows/BIRDMAn%20CI/badge.svg)](https://github.com/gibsramen/BIRDMAn/actions)
[![GitHub Actions CI](https://github.com/biocore/birdman/workflows/BIRDMAn%20CI/badge.svg)](https://github.com/biocore/BIRDMAn/actions)
[![Documentation Status](https://readthedocs.org/projects/birdman/badge/?version=stable)](https://birdman.readthedocs.io/en/stable/?badge=stable)
[![PyPI](https://img.shields.io/pypi/v/birdman.svg)](https://pypi.org/project/birdman)
[![DOI](https://zenodo.org/badge/312046610.svg)](https://zenodo.org/badge/latestdoi/312046610)
Expand All @@ -11,7 +11,9 @@ See the [documentation](https://birdman.readthedocs.io/en/stable/?badge=stable)

## Installation

Currently BIRDMAn requires Python 3.7 or higher.
Currently BIRDMAn requires Python 3.8 or higher.

We recommend using [mamba](https://github.com/mamba-org/mamba) for installation of dependencies.

```bash
conda install -c conda-forge biom-format patsy xarray arviz cmdstanpy
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1 change: 1 addition & 0 deletions pytest.ini
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@@ -1,3 +1,4 @@
[pytest]
filterwarnings =
ignore::DeprecationWarning
ignore::FutureWarning
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